Stephen E. Saunders was a former MI6 agent and SAS soldier. While working with Jack Bauer on Operation Nightfall, he was abandoned in enemy territory by the Delta Force team and was presumed dead for several years. Eventually he contacted his daughter Jane and returned to the United States. Following Nightfall he became involved in bio-terrorist activity, and masterminded a plot in which he could hold the entire US hostage with an extremely contagious and lethal virus.

Bauer was ordered to gather a six-man team that would infiltrate Kosovo by air, eliminate the threat posed by Drazen, and move to a distant extraction point where they would be extracted by a helicopter. MI6 loaned Saunders to the United States for the operation.

During the mission, things went wrong and an explosion ending up killing not only Drazen but his wife and daughter as well. Bauer's team was ambushed and he thought he was the only one to survive the operation. It was later revealed in Day 1 Drazen's body double was killed in explosion, not Victor himself.

Saunders was held prisoner and tortured by the Bosnian secret police for two years, and the US government refused to negotiate to get him released. Eventually Saunders was freed and he lived a life in England. Four years prior to the events that took place in Day 3, Saunders contacted his daughter Jane. His wife died six months prior to the time he contacted Jane.

Stephen Saunders acquired the Cordilla virus from his associate Michael Amador. When Amador was captured by CTU, but then apparently escaped, he contacted Saunders for help with fleeing the country. Saunders asked him if one of the CTU agents was Jack Bauer; when Amador confirmed this, Saunders knew that Bauer could not be so easily outsmarted, and that Amador was being carefully tracked. Saunders sent a subordinate named Dorman with a briefcase for Amador, but when it was opened, a bomb inside was triggered and it blew up both men.

Saunders first demand was to have Secret Service pick up a package and bring it to Palmer. After Aaron Pierce proved the package was safe, Palmer discovered a non-traceable phone. Saunders called him and told him this would be their way of communicating with each other. His second demand was for Palmer to hold a press conference, on any political issue, and use the phrase "the sky is falling" somewhere in his speech. The President followed through with this demand also.

When Ryan Chappelle began to run money traces, Saunders saw this as a threat to him and he wanted Chappelle dead. Saunders contacted Palmer and ordered the execution of Chappelle, or he would infect another city. He gave Palmer a location where Chappelle's body was to be given to his men by 7 a.m. After struggling with the decision, Palmer was forced to agree to buy CTU more time and had Jack Bauer carry out the task.

CTU Los Angeles was able to trace Saunders' location and Chase Edmunds ran the operation, while Jack used a helicopter to transport Chappelle to the junkyard. When Chase learned that Saunders was using a device to relay calls from the location, and that their lead was a dead end, Jack was forced to go through with the execution. Saunder's men took Chappelle's body into their van, and one of them confirmed for Saunders that the corpse belonged to Ryan, while Jack had no choice but to head back to CTU.

Saunders' next demand to Palmer was a list of covert US agents posing as citizens in numerous countries. Palmer would not go with this demand. When CTU learned that Saunders had a daughter, they grabbed Jane and began interrogating her. Jane revealed that she has a private number to contact Saunders if it was an emergency. When it became apparent that Jane had no more useful information, Jack had Jane call Saunders on his private line. As Saunders was in the process of ordering Ian, his courier in San Francisco, to infect the population there due to Palmer not cooperating with his demands, he stops due to the ring of the private line cell phone for Jane. As he picked up Jane's call, his associate Osterlind discovered the call was being monitored. Saunders told Jane that he wanted to speak with Jack. Saunders threaten Jack telling him what he is capable of. As Jack responded back of what he is capable of, with Saunders knowing that he meant threatening to hurt Jane, Adam Kaufman and Chloe O'Brian were able to close-in on Stephen's real hideout.

Osterlind insisted on leaving the building, but Saunders was convinced that CTU would use satellite to pick up on their location. When Osterlind refused to stay, Saunders shot and killed him. He then patiently waited for CTU to arrive and corner the building.

After Jack Bauer demanded for Saunders to surrender, Saunders called Tony Almeida, the Special Agent in Charge of CTU Los Angeles. Saunders demanded for Tony to clear a path for him, to which Tony questioned why he would carry out such an outrageous demand. Saunders then provided proof that his men had captured his wife, Michelle Dessler, after she left the Chandler Plaza Hotel, and threatened to take her eye out if Tony didn't meet his demands.

Tony was forced to comply, and he ordered Agent Tom Baker to follow a Code 9 and move everyone into the front. After Baker lead everybody away, Saunders walked out of the building and successfully escaped. After getting to a safe location, Saunders called Tony and asked for him to deliver Jane Saunders to him. He said he would call back with further instructions.

After stepping down as the CTU director and letting Jack take over the operation, Tony grabbed Jane Saunders and began to escort her out of the building. When Chloe told Jack that Saunders had Michelle, Jack ordered a lockdown, but Tony managed to get to the garage and escape. With help from satellite, Jack was able to catch Tony and convince him to work along with CTU.

Tony went through with the trade off, and Michelle was exchanged for Jane. Not wanting to go with her father's men, Jane began to run away, causing Saunders to expose himself in an attempt to call her back. Now having a visual confirmation on Saunders, CTU and other law enforcement agents burst onto the scene and a shootout began. In the midst of the chaos Saunders managed to run off. Chase, Tony, and the rest of CTU handled the hostiles, while Jack chased after Saunders.

A helicopter arrived to pick up Saunders and opened fire at Jack, forcing him to take cover. Fortunately, a fighter jet arrived and took out the helicopter, successfully preventing Saunder's escape. Bauer was able to bring Saunders into custody and demanded the location of the remaining vials. When Saunders refused to cooperate, Jack brought Saunders and Jane to the Chandler Plaza Hotel where the first vial had been released. Jack was able to force Saunders to comply by threatening to send Jane inside the hotel, where she would be infected with the virus.

Eventually all but one of the vials around the country were neutralized. Saunders identified the last remaining courier as Arthur Rabens, who was located in Los Angeles. While looking through photos of people in a subway, Theresa Ortega arrived at CTU. She was mourning the death of her husband Gael, who sacrificed his life to help the people in the Chandler Plaza Hotel. Before Saunders could identify Rabens, Theresa shot him twice in the chest at close range with a pistol she discovered in Gael's desk. Theresa was then subdued by CTU security. Michelle Dessler and the officer guarding Saunders attempted to revive him, however he quickly succumbed to his wounds just as Rabens' picture came up.

It is said in the show that Stephen was tortured by Bosnian secret police which is probably a writers mistake. Bosnia was a USA ally and he was probably tortured by Serbian police or Bosnian Serb police (Republika Srpska).

Saunders turned out to be correct when he predicted that Jack would be abandoned by his government, just as Saunders had been. At the end of Season 4, Jack had to fake his death to trick White House Chief of StaffWalt Cummings, who targeted him for assassination. Then, during Season 5, he was a central target of the Sentox nerve gas conspiracy which was sponsored by numerous members of the executive branch (including Cummings and PresidentCharles Logan), and was turned over to Cheng Zhi to be tortured for 20 months. Later during Season 7 Jack was hauled to a hearing in front of the United States Senate for his use of torture on suspects. Finally during Season 8, he was again betrayed by a sitting President (this time Allison Taylor), who first turned him over to mercenaries to be murdered, then left him to fend for himself as an international fugitive.